Amorphous carbon (a-C) thin films have various useful properties; thus, their applications are wide-ranging. These properties are characterized by the ratio of sp3 to sp2 carbon in the thin film, and many studies have been reported on changing this ratio. In this paper, we used an F2 laser with a wavelength of 157 nm to photoexcite the surface of an a-C thin film, and simultaneously photodecompose atmospheric oxygen molecules O2 into excited singlet oxygen atoms O(1D). The results showed that O(1D) atoms can photochemically etch sp2 carbon in thin films significantly better than triplet oxygen atoms O(3P). Thus, we found that the surface layer of the a-C thin film was photochemically modified to be transparent. Raman spectroscopy revealed no change in the chemical bonding state of the transparently modified a-C thin film. On the other hand, in X-ray photoelectron spectroscopy, the intensity of the C 1s peak originated to sp2 carbon decreased. The refractive index was also slightly lowered, probably due to lowering film density. In addition, droplets mainly composed of sp2 carbon generated during thin film deposition were significantly removed after F2 laser irradiation. The electrical resistivity slightly decreased upon F2 laser irradiation and remarkably decreased as the substrate was heated, exhibiting low bandgap properties. Therefore, we succeeded in discovering a new method for changing the ratio of sp3 to sp2 carbon in a-C to be transparent thin film by preferentially generating O(1D) atoms using the F2 laser, as a new elemental technology for fabricating transparent flexible electronic devices.